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12-09-2009, 08:41 AM
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#1 |
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Junior Member
Location: oxford Join Date: Aug 2008
Posts: 5
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MAQ and SNP calling
Hello,
I've used MAQ to call SNPs in Illumina data, it worked fine apart from the read depth. When I looked at the alignment using IGV the read depth is often alot more. Im sure theres a reason, can anyone tell me why?. Thank you |
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12-09-2009, 04:48 PM
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Nils Homer
Location: Boston, MA, USA Join Date: Nov 2008
Posts: 1,285
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12-10-2009, 02:21 AM
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#3 |
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Member
Location: it Join Date: Oct 2009
Posts: 40
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can any one tell me the details regarding the alignment output of maq
Last edited by bioenvisage; 12-10-2009 at 02:35 AM. |
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12-11-2009, 09:23 AM
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#4 | |
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Member
Location: Sydney, Australia Join Date: Jul 2009
Posts: 14
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Quote:
Well, the maq map output itself is binary. You can run the pileup command to give you the read bases and the quality at each position. Check the maq documentation and that should elaborate further what the columns in the output are. BertieW |
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